B final

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Aug 28, 2011 · e159e5b · e159e5b
1 parent 517dd0c
commit e159e5b
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diff --git a/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java b/src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
@@ -238,6 +238,10 @@ private IAtomType perceiveBorons(IAtomContainer atomContainer, IAtom atom)
 	        atomContainer.getConnectedAtomsCount(atom) <= 4) {
 	        IAtomType type = getAtomType("B.minus");
 	        if (isAcceptable(atom, atomContainer, type)) return type;
+	    } else if (atom.getFormalCharge() == +3
+                && atomContainer.getConnectedAtomsCount(atom) == 4) {
+            IAtomType type = getAtomType("B.3plus");
+            if (isAcceptable(atom, atomContainer, type)) return type;
 	    } else if (atomContainer.getConnectedAtomsCount(atom) <= 3) {
 	        IAtomType type = getAtomType("B");
 	        if (isAcceptable(atom, atomContainer, type)) return type;

diff --git a/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl b/src/main/org/openscience/cdk/dict/data/cdk-atom-types.owl
@@ -1792,6 +1792,15 @@
     <at:piBondCount>0</at:piBondCount>
     <at:hybridization rdf:resource="&at;sp3"/>
   </at:AtomType>
+
+    <at:AtomType rdf:ID="B.3plus">
+    <at:formalCharge>3</at:formalCharge>
+    <at:hasElement rdf:resource="&elem;B"/>
+    <at:formalNeighbourCount>4</at:formalNeighbourCount>
+    <at:lonePairCount>0</at:lonePairCount>
+    <at:piBondCount>0</at:piBondCount>
+    <at:hybridization rdf:resource="&at;sp3"/>
+    </at:AtomType> 
 
 <at:AtomType rdf:ID="Rb.plus">
     <at:formalCharge>1</at:formalCharge>

diff --git a/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java b/src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
@@ -3646,6 +3646,40 @@ public void testPentaMethylPhosphane() throws Exception {
         assertAtomTypes(testedAtomTypes, expectedTypes, mol);
     }
 
+
+    @Test
+    public void test_B_3plus() throws Exception {
+        IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
+        IMolecule mol = builder.newInstance(IMolecule.class);
+        IAtom a1 = builder.newInstance(IAtom.class,"B");
+        a1.setFormalCharge(3);
+        mol.addAtom(a1);
+        IAtom a2 = builder.newInstance(IAtom.class,"C");
+        a2.setFormalCharge(0);
+        mol.addAtom(a2);
+        IAtom a3 = builder.newInstance(IAtom.class,"C");
+        a3.setFormalCharge(0);
+        mol.addAtom(a3);
+        IAtom a4 = builder.newInstance(IAtom.class,"C");
+        a4.setFormalCharge(0);
+        mol.addAtom(a4);
+        IAtom a5 = builder.newInstance(IAtom.class,"C");
+        a5.setFormalCharge(0);
+        mol.addAtom(a5);
+        IBond b1 = builder.newInstance(IBond.class,a1, a2, IBond.Order.SINGLE);
+        mol.addBond(b1);
+        IBond b2 = builder.newInstance(IBond.class,a1, a3, IBond.Order.SINGLE);
+        mol.addBond(b2);
+        IBond b3 = builder.newInstance(IBond.class,a1, a4, IBond.Order.SINGLE);
+        mol.addBond(b3);
+        IBond b4 = builder.newInstance(IBond.class,a1, a5, IBond.Order.SINGLE);
+        mol.addBond(b4);
+
+
+        String[] expectedTypes = {"B.3plus", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
+        assertAtomTypes(testedAtomTypes, expectedTypes, mol);
+    }
+
     @Test
     public void test_Te_4plus() throws Exception {
         IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();